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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement | |||||||||
![]() | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement unsharpened map | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Dang HV / Veesler D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection. Authors: Nataly Kacherovsky / Lucy F Yang / Ha V Dang / Emmeline L Cheng / Ian I Cardle / Alexandra C Walls / Matthew McCallum / Drew L Sellers / Frank DiMaio / Stephen J Salipante / Davide Corti / ...Authors: Nataly Kacherovsky / Lucy F Yang / Ha V Dang / Emmeline L Cheng / Ian I Cardle / Alexandra C Walls / Matthew McCallum / Drew L Sellers / Frank DiMaio / Stephen J Salipante / Davide Corti / David Veesler / Suzie H Pun / ![]() ![]() Abstract: The coronavirus disease 2019 (COVID-19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for ...The coronavirus disease 2019 (COVID-19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for distinct viral proteins are critical components for rapid diagnostics and targeted therapeutics. In this work, we demonstrate the selection of novel DNA aptamers that bind to the SARS-CoV-2 spike glycoprotein with high specificity and affinity (<80 nM). Through binding assays and high resolution cryo-EM, we demonstrate that SNAP1 (SARS-CoV-2 spike protein N-terminal domain-binding aptamer 1) binds to the S N-terminal domain. We applied SNAP1 in lateral flow assays (LFAs) and ELISAs to detect UV-inactivated SARS-CoV-2 at concentrations as low as 5×10 copies mL . SNAP1 is therefore a promising molecular tool for SARS-CoV-2 diagnostics. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 122.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 60.7 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() | 618.8 KB 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 981.5 KB | Display | ![]() |
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Full document | ![]() | 981 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: SARS-CoV-2 S/S2M11/SNAP1 Local Refinement locally-filtered map
File | emd_24679_additional_1.map | ||||||||||||
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Annotation | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement locally-filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 S/S2M11/SNAP1 Local Refinement half map 1
File | emd_24679_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 S/S2M11/SNAP1 Local Refinement half map 2
File | emd_24679_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 S/S2M11/SNAP1 Local Refinement half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1
Entire | Name: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1 |
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Components |
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-Supramolecule #1: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1
Supramolecule | Name: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 142 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: TBS pH 8.0, 25mM Tris-HCl, 150mM NaCl and 0.1% octyl-glucoside | ||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55369 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |